Assigning SNPs to Genes and Gene Regions — the ALIGATOR way

By principal various people doing this differently based on a different sets of (known/consensus) gene list. In the paper by Holmans, et al 2009 describing the “ALIGATOR” program to perform Gene ontology Analysis of GWAS,

1. “seq-gene” containing the list of genes can be downloaded from

2. Pseudo genes containing “pseudo” in the “feature_id” are excluded

3. Extract records with “feature_type” : “gene”, “group_label” : “”reference”, and “tax_id” : “9606”.

4. Retain these fields: chromosome, chr_start, chr_stop, and feature_id (NCBI gene ID)

5. SNP ID and chromosomal location are compared to the file from (4) ==> This is the hard part to be continued.